fatal error in autodock

Hello everyone

I am facing fatal error when I am running autoduck4. Please suggest me how I can fix this error

C:/Users/Public/Autodocking/autodock4: FATAL ERROR: C:/Users/Public/Autodocking/autodock4: ERROR:  All ATOM and HETATM records must be given before any nested BRANCHes; see line 25 in PDBQT file "ligand.pdbqt".
C:/Users/Public/Autodocking/autodock4: Unsuccessful Completion.

autodock

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updated 3.2 years ago by Ram

• written 4.2 years ago by sumaiya •

1 answer

You are not being very helpful to us. Any time your problem is explained in a single sentence or two, chances are that you didn't provide enough detail to help us help you.

Some basic things: what is the command you entered when the error occurred? Did you look into your ligand file?

ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 25 in PDBQT file "ligand.pdbqt".

This is a pretty clear error message - it says that ATOM lines must come before BRANCH lines. Is that the case in your ligand file, and if not, how did you make that file?

If you actually did all of this (the error is clear as to which file is wrong) and entered the required information in your question, we'd be answering it instead of breaking down the error message word by word.

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written 4.2 years ago by Mensur Dlakic

first i prepare pdbqt file of ligand and protein then prepare gpf file, dpf file. after that i run autogrid diretctly ( Run>autogrid), than(run>autodock4)....i am facing this issue its my ligand.pdbqt file

REMARK 5 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: O2_2 and C9_9 REMARK 2 A between atoms: O3_3 and C10_10 REMARK 3 A between atoms: O4_4 and C13_13 REMARK 4 A between atoms: N7_7 and C11_11 REMARK 5 A between atoms: C12_12 and C13_13 ROOT HETATM 1 O1 SUB 1 -1.365 -0.541 1.022 0.00 0.00 -0.353 OA HETATM 2 C9 SUB 1 -1.367 0.971 -0.802 0.00 0.00 0.198 C HETATM 3 C10 SUB 1 -2.797 0.576 -0.499 0.00 0.00 0.182 C HETATM 4 C11 SUB 1 -0.654 0.585 0.482 0.00 0.00 0.263 C HETATM 5 C12 SUB 1 -2.610 -0.701 0.308 0.00 0.00 0.179 C ENDROOT BRANCH 4 6 HETATM 6 N7 SUB 1 0.713 0.210 0.259 0.00 0.00 -0.280 N HETATM 7 C14 SUB 1 1.741 1.172 0.398 0.00 0.00 0.331 A HETATM 8 O5 SUB 1 1.541 2.348 0.709 0.00 0.00 -0.246 OA HETATM 9 N8 SUB 1 3.037 0.698 0.156 0.00 0.00 -0.275 N HETATM 10 C17 SUB 1 3.397 -0.594 -0.198 0.00 0.00 0.250 A HETATM 11 O6 SUB 1 4.549 -0.963 -0.401 0.00 0.00 -0.268 OA HETATM 12 C16 SUB 1 2.265 -1.535 -0.322 0.00 0.00 0.092 A HETATM 13 C15 SUB 1 1.025 -1.098 -0.094 0.00 0.00 0.104 A ENDBRANCH 4 6 HETATM 14 O2 SUB 1 -1.243 2.347 -1.101 0.00 0.00 -0.388 OA BRANCH 5 15 HETATM 15 C13 SUB 1 -2.503 -1.950 -0.557 0.00 0.00 0.198 C HETATM 16 O4 SUB 1 -2.322 -3.073 0.288 0.00 0.00 -0.398 OA ENDBRANCH 5 15 HETATM 17 O3 SUB 1 -3.409 1.547 0.350 0.00 0.00 -0.390 OA TORSDOF 5

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written 4.2 years ago by sumaiya •

It is impossible to read through your ligand file because it is not properly formatted. Please tell me which line in that file is 25th based on what you provided?

When you paste the lines that need to be formatted, you select them and click on the button that says 101010 which will format them. When it looks like the .pdbqt file I pasted below, it is much easier to inspect the contents.

REMARK  12 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: C2'_10  and  O2'_11
REMARK    2  A    between atoms: C1'_13  and  N9_14
REMARK    3  A    between atoms: C6_19  and  N6_20
REMARK    4  A    between atoms: C2'_38  and  O2'_39
REMARK    5  A    between atoms: C1'_41  and  N9_42
REMARK    6  A    between atoms: C6_47  and  N6_48
REMARK    7  A    between atoms: C2'_66  and  O2'_67
REMARK    8  A    between atoms: C1'_69  and  N9_70
REMARK    9  A    between atoms: C6_75  and  N6_76
REMARK   10  A    between atoms: C2'_94  and  O2'_95
REMARK   11  A    between atoms: C1'_97  and  N9_98
REMARK   12  A    between atoms: C6_103  and  N6_104
ROOT
ATOM      1  P     A C   1     -15.532 -69.520  -2.464  1.00125.22     0.408 P
ATOM      2  OP1   A C   1     -15.575 -69.043  -3.862  1.00124.72    -0.624 OA
ATOM      3  OP2   A C   1     -14.759 -68.759  -1.457  1.00121.99    -0.624 OA
ATOM      4  O5'   A C   1     -15.020 -71.056  -2.479  1.00129.94    -0.287 OA
ATOM      5  C5'   A C   1     -13.732 -71.415  -2.993  1.00130.77     0.216 C
ATOM      6  C4'   A C   1     -12.700 -71.194  -1.902  1.00132.63     0.180 C
ATOM      7  O4'   A C   1     -13.108 -71.866  -0.671  1.00133.57    -0.353 OA
ATOM      8  C3'   A C   1     -11.351 -71.808  -2.297  1.00133.33     0.198 C
ATOM      9  O3'   A C   1     -10.322 -70.839  -2.045  1.00131.78    -0.279 OA
ATOM     10  C2'   A C   1     -11.222 -72.966  -1.338  1.00133.85     0.199 C
ATOM     11  C1'   A C   1     -11.865 -72.337  -0.114  1.00135.60     0.262 C
ATOM     12  P     A C   2      -9.044 -70.710  -2.990  1.00132.86     0.408 P
ATOM     13  OP1   A C   2      -8.592 -72.069  -3.367  1.00131.82    -0.624 OA

From what I can tell, your ligand has no ATOM lines, which is probably why it doesn't work. My guess is that the initial PDB file from which you extracted the ligand was incorrect, but really tough to tell based on the limited information you provided.

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written 4.2 years ago by Mensur Dlakic

REMARK  5 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: O2_2  and  C9_9 
REMARK    2  A    between atoms: O3_3  and  C10_10 
REMARK    3  A    between atoms: O4_4  and  C13_13 
REMARK    4  A    between atoms: N7_7  and  C11_11 
REMARK    5  A    between atoms: C12_12  and  C13_13 
ROOT
HETATM    1  O1  SUB     1      -1.365  -0.541   1.022  0.00  0.00    -0.353 OA
HETATM    2  C9  SUB     1      -1.367   0.971  -0.802  0.00  0.00     0.198 C 
HETATM    3  C10 SUB     1      -2.797   0.576  -0.499  0.00  0.00     0.182 C 
HETATM    4  C11 SUB     1      -0.654   0.585   0.482  0.00  0.00     0.263 C 
HETATM    5  C12 SUB     1      -2.610  -0.701   0.308  0.00  0.00     0.179 C 
ENDROOT
BRANCH   4   6
HETATM    6  N7  SUB     1       0.713   0.210   0.259  0.00  0.00    -0.280 N 
HETATM    7  C14 SUB     1       1.741   1.172   0.398  0.00  0.00     0.331 A 
HETATM    8  O5  SUB     1       1.541   2.348   0.709  0.00  0.00    -0.246 OA
HETATM    9  N8  SUB     1       3.037   0.698   0.156  0.00  0.00    -0.275 N 
HETATM   10  C17 SUB     1       3.397  -0.594  -0.198  0.00  0.00     0.250 A 
HETATM   11  O6  SUB     1       4.549  -0.963  -0.401  0.00  0.00    -0.268 OA
HETATM   12  C16 SUB     1       2.265  -1.535  -0.322  0.00  0.00     0.092 A 
HETATM   13  C15 SUB     1       1.025  -1.098  -0.094  0.00  0.00     0.104 A 
ENDBRANCH   4   6
HETATM   14  O2  SUB     1      -1.243   2.347  -1.101  0.00  0.00    -0.388 OA
BRANCH   5  15
HETATM   15  C13 SUB     1      -2.503  -1.950  -0.557  0.00  0.00     0.198 C 
HETATM   16  O4  SUB     1      -2.322  -3.073   0.288  0.00  0.00    -0.398 OA
ENDBRANCH   5  15
HETATM   17  O3  SUB     1      -3.409   1.547   0.350  0.00  0.00    -0.390 OA
TORSDOF 5

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written 4.2 years ago by sumaiya •

It is too time-consuming when we have to troubleshoot everything one thing at a time, especially when you are not responding to my questions and suggestions. You will have to figure this one out on your own.

I will repeat: it is likely to be an issue with your original PDB ligand file, or whatever was used to make ligand.pdbqt. That file has only HETATM lines, which is clearly wrong because carbons, oxygens and nitrogens are not heteroatoms. Besides, that SUB in place of chain and residue identifiers is likely to be wrong as well. You have above how a proper ligand file should look like, so I suggest you work with your input until you can get something similar to it. Maybe replacing HETATM with ATOM will fix it. In case it is not clear, there should be two empty spaces after ATOM to make the number of characters equal after replacement.

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written 4.2 years ago by Mensur Dlakic